Package Details: samtools 1.9-1

Git Clone URL: (read-only)
Package Base: samtools
Description: tools for manipulating next-generation sequencing data
Upstream URL:
Licenses: custom
Submitter: Vrob
Maintainer: viralstitch
Last Packager: alexpe87
Votes: 27
Popularity: 0.417968
First Submitted: 2009-11-04 21:48
Last Updated: 2018-07-20 08:24

Latest Comments

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MikeDacre commented on 2014-09-11 22:23

This package does not allow the successful compilation of cufflinks. In order for cufflinks to work all of the header files have to be included.

Adding the following lines to package() solves the problem:

mkdir -p "$pkgdir/usr/include/bam"

install -Dm644 $srcdir/$pkgname-$pkgver/*.h "$pkgdir/usr/include/bam"

Rhinoceros commented on 2014-08-20 10:37

I'm really not sure. I wouldn't know where to look, either.

wookietreiber commented on 2014-08-19 06:06

Do pacaur and packer use different compiler options? IIRC /etc/makepkg.conf should be the place where to set up your arch linux compilation ...

Rhinoceros commented on 2014-08-19 06:02

That's quite odd. I wanted to come back and report how I installed it. I tried `pacaur -Syu` and it failed twice. I then tried it with `packer -Syu`, and it now installed fine. Sorry for the noise, although it's quite odd that one worked and the other failed. (FWIW I had python2 but not luaji.)

wookietreiber commented on 2014-08-19 05:57

Did you install all the optional dependencies?

Would you please give more specific information about these failed tests?

Rhinoceros commented on 2014-08-19 05:17

Is any one else having troubles with installation? It fails with:

> Number of tests:
> total .. 375
> passed .. 339
> failed .. 2
> expected failure .. 34
> unexpected pass .. 0
> Makefile:172: recipe for target 'check' failed
> make: *** [check] Error 1
> ==> ERROR: A failure occurred in check().
> Aborting...

I scanned the tests above this, but could find nothing unusual.

lqs commented on 2013-12-16 07:10

Glad to see bio-software(or NGS program, like bwa, samtools).

Maybe we should catalog those software more specify so anybody can find it easily.

Thanks ^_^

wookietreiber commented on 2013-11-21 16:31


stratust commented on 2013-11-21 16:13

Hi wookietreiber,

I've been too busy lately to take care of this package.
Feel free to adopt it!

wookietreiber commented on 2013-11-21 10:26

Hi, I have tried to sanitize the PKGBUILD, have a look:

I have added your original, so you can view the diff:

Would be nice if you could replace this with the current build.